I'm not sure about the right questions, but it is important that the questions be asked at the right time and place, by the right person.
Before most employees will open up with honest feedback they have to be ASSURED that their responses cannot be identified and will not get back to management in an identifiable form.
Questions that I might consider may include;
1. Is there a good professional trust between you and the person responsible for your appraisal?
1b. If not, what are some of the issues?
2Do you feel that your appraisal helps you to identify areas for further growth and development?
2b. Does the appraisal help to identify support mechanisms and resources for your professional development?
3.What are some of the topics/issues you would like the appraisal to address, that it doesn't address at the moment?
Basically, if the employee feels that there is nothing in the process of benefit to them, the appraisal is merely a mild form of torture they have to endure with mock sincerity and some good play-acting : )